source code for mothur


I am trying to compile mothur from the source code. I am running into difficulty because whenever the blast program is being invoked, it is searching for older versions of BLAST executibles, such as “blastall.exe”, “formatdb.exe”, “megablast.exe”. Is there plans to update these to the newer versions of the Blast modules provided by NCBI, or do I have to download these and install them separately in a location of my choice?

If so, where would I obtain these from an old version of BLAST, and which version would be best?

The reason I am asking is that we do not have older versions of the Stand Alone Blast program installed on our system, so we cannot designate an alternative path to these files.



The older versions of blast are available with mothur’s executable versions. The blast folder is inside the mothur folder, along with the catchall executable and uchime executable.


Ah but that is not necessarily clear to those compiling the data from source (I was assuming that all the executibles would be present in the source code) onto our main computer.

Thanks for clarifying that and I will let them know where they can locate it. I assume that they should rename the folder to “bin”, and place it in the same folder that mothur is executed from, correct?


Sorry for the confusion. No, just move the entire blast folder to wherever you are putting mothur’s executable. Mothur will look for the blast executables in blast/bin. The reason we don’t include the blast executables with the source is because the blast executables are system dependent and the source is not.